I am by no means an expert here, but it may have something to do with the way the .desktop file is structured (/usr/share/applications/hildon/email-engine.desktop). There's an entry for "StartupWMClass=ossemail" which I think is used for window notification/communication. I don't know how to "pass" this value to the application via the command line. But this may be the reason why Simple-Launcher can run the default email application correctly. Perhaps looking at the code for simple-launcher can shed some light on this issue.